Coralline algae (Rhodophyta) in a changing world: integrating ecological,physiological, and geochemical responses to global change

Coralline algae are globally distributed benthic primary producers that secrete calcium carbonate skeletons. In the context of ocean acidification, they have received much recent attention due to the potential vulnerability of their high‐Mg calcite skeletons and their many important ecological roles. Herein, we summarize what is known about coralline algal ecology and physiology, providing context to understand their responses to global climate change. We review the impacts of these changes, including ocean acidification, rising temperatures, and pollution, on coralline algal growth and calcification. We also assess the ongoing use of coralline algae as marine climate proxies via calibration of skeletal morphology and geochemistry to environmental conditions. Finally, we indicate critical gaps in our understanding of coralline algal calcification and physiology and highlight key areas for future research. These include analytical areas that recently have become more accessible, such as resolving phylogenetic relationships at all taxonomic ranks, elucidating the genes regulating algal photosynthesis and calcification, and calibrating skeletal geochemical metrics, as well as research directions that are broadly applicable to global change ecology, such as the importance of community‐scale and long‐term experiments in stress response.     

RNA viruses in the sea

Viruses are ubiquitous in the sea and appear to outnumber all other forms of marine life by at least an order of magnitude. Through selective infection, viruses influence nutrient cycling, community structure, and evolution in the ocean. Over the past 20 years we have learned a great deal about the diversity and ecology of the viruses that constitute the marine virioplankton, but until recently the emphasis has been on DNA viruses. Along with expanding knowledge about RNA viruses that infect important marine animals, recent isolations of RNA viruses that infect single-celled eukaryotes and molecular analyses of the RNA virioplankton have revealed that marine RNA viruses are novel, widespread, and genetically diverse. Discoveries in marine RNA virology are broadening our understanding of the biology, ecology, and evolution of viruses, and the epidemiology of viral diseases, but there is still much that we need to learn about the ecology and diversity of RNA viruses before we can fully appreciate their contributions to the dynamics of marine ecosystems. As a step toward making sense of how RNA viruses contribute to the extraordinary viral diversity in the sea, we summarize in this review what is currently known about RNA viruses that infect marine organisms.     

Exploring novel bioactive compounds from marine microbes

The historical paradigm of the deep ocean as a biological 'desert' has shifted to one of a 'rainforest' owing to the isolation of many novel microbes and their associated bioactive compounds. Recently, there has been an explosion of information about novel bioactive compounds that have been isolated from marine microbes in an effort to further explore the relatively untapped marine microbes and their secondary metabolites for drug discovery. The microbes are recovered and purified from the ocean by both conventional and innovative isolation methods to obtain those previously thought to be 'uncultivable'. To overcome the difficulties and limitations associated with cultivation techniques, several DNA-based molecular methods have been developed to bypass the culture-dependent bottleneck. Bioactive compounds isolated using the above strategies have not only shown importance in biotechnological and pharmaceutical applications but have also increased our understanding of the diversity of marine microbiota, ecosystem functions and the exploitable biology.     

Diversity and evolution of marine phytoplankton

Marine phytoplankton organisms account for more than 45% of the photosynthetic net primary production on Earth. They are distributed across many of the major clades of the tree of life and include prokaryotes, and eukaryotes that acquired photosynthesis through the process of endosymbiosis. If the number of extant described species is relatively low compared to the diversity of the terrestrial plants, recent insights into the genetic diversity of natural assemblages have revealed a large unsuspected diversity at different taxonomic levels. Wide infra-specific diversity is also being discovered in many widespread and well known morphological species. This review summarizes data obtained in the fields of ecology, evolutionary biology, physiology and genomics that have improved our understanding of the biodiversity and evolution of marine phytoplankton. To cite this article: N. Simon et al., C. R. Biologies 332 (2009).     

Vertical distribution of picoeukaryotic diversity in the Sargasso Sea

Eukaryotic molecular diversity within the picoplanktonic size-fraction has primarily been studied in marine surface waters. Here, the vertical distribution of picoeukaryotic diversity was investigated in the Sargasso Sea from euphotic to abyssal waters, using size-fractionated samples (< 2 microm). 18S rRNA gene clone libraries were used to generate sequences from euphotic zone samples (deep chlorophyll maximum to the surface); the permanent thermocline (500 m); and the pelagic deep-sea (3000 m). Euphotic zone and deep-sea data contrasted strongly, the former displaying greater diversity at the first-rank taxon level, based on 232 nearly full-length sequences. Deep-sea sequences belonged almost exclusively to the Alveolata and Radiolaria, while surface samples also contained known and putative photosynthetic groups, such as unique Chlorarachniophyta and Chrysophyceae sequences. Phylogenetic analyses placed most Alveolata and Stramenopile sequences within previously reported 'environmental' clades, i.e. clades within the Novel Alveolate groups I and II (NAI and NAII), or the novel Marine Stramenopiles (MAST). However, some deep-sea NAII formed distinct, bootstrap supported clades. Stramenopiles were recovered from the euphotic zone only, although many MAST are reportedly heterotrophic, making the observed distribution a point for further investigation. An unexpectedly high proportion of radiolarian sequences were recovered. From these, five environmental radiolarian clades, RAD-I to RAD-V, were identified. RAD-IV and RAD-V were composed of Taxopodida-like sequences, with the former solely containing Sargasso Sea sequences, although from all depth zones sampled. Our findings highlight the vast diversity of these protists, most of which remain uncultured and of unknown ecological function.     

Deviations in skeletons of radiolarians

Deviations in the skeleton structure of radiolarians are extremely rare in the fossil record. They are known from the Devonian to Recent. This is a very ancient and periodically repeated phenomenon, which should be regarded as a regularity or “lost chance” rather than exotic or accident. Emergence of deviant “mutants” in radiolarians is probably connected with two main causes, i.e., disturbance during reproduction and mutations in particular modules. From the point of view of the morphogenesis of skeletal structures, deviancy facilitates the recognition of relatively “weak” modules–blocks in the general skeleton pattern, which are subject to structural changes. Nonheritable deviant variants have been revealed in skeletons of 61 radiolarian in all of three subphyla of the phylum Radiolaria: Polycystina, Phaeodaria, and Collodaria. Three deviant types are recognized: multiplicative, posterioric and supplemental.     

The biology and ecology of the ocean sunfish <Emphasis Type="Italic">Mola mola</Emphasis>: a review of current knowledge and future research perspectives

Relatively little is known about the biology and ecology of the world’s largest (heaviest) bony fish, the ocean sunfish Mola mola, despite its worldwide occurrence in temperate and tropical seas. Studies are now emerging that require many common perceptions about sunfish behaviour and ecology to be re-examined. Indeed, the long-held view that ocean sunfish are an inactive, passively drifting species seems to be entirely misplaced. Technological advances in marine telemetry are revealing distinct behavioural patterns and protracted seasonal movements. Extensive forays by ocean sunfish into the deep ocean have been documented and broad-scale surveys, together with molecular and laboratory based techniques, are addressing the connectivity and trophic role of these animals. These emerging molecular and movement studies suggest that local distinct populations may be prone to depletion through bycatch in commercial fisheries. Rising interest in ocean sunfish, highlighted by the increase in recent publications, warrants a thorough review of the biology and ecology of this species. Here we review the taxonomy, morphology, geography, diet, locomotion, vision, movements, foraging ecology, reproduction and species interactions of M. mola. We present a summary of current conservation issues and suggest methods for addressing fundamental gaps in our knowledge.     

Radiolaria divided into Polycystina and Spasmaria in combined 18S and 28S rDNA phylogeny

Radiolarians are marine planktonic protists that belong to the eukaryote supergroup Rhizaria together with Foraminifera and Cercozoa. Radiolaria has traditionally been divided into four main groups based on morphological characters; i.e. Polycystina, Acantharia, Nassellaria and Phaeodaria. But recent 18S rDNA phylogenies have shown that Phaeodaria belongs within Cerocozoa, and that the previously heliozoan group Taxopodida should be included in Radiolaria. 18S rDNA phylogenies have not yet resolved the sister relationship between the main Radiolaria groups, but nevertheless suggests that Spumellaria, and thereby also Polycystina, are polyphyletic. Very few sequences other than 18S rDNA have so far been generated from radiolarian cells, mostly due to the fact that Radiolaria has been impossible to cultivate and single cell PCR has been hampered by low success rate. Here we have therefore investigated the mutual evolutionary relationship of the main radiolarian groups by using the novel approach of combining single cell whole genome amplification with targeted PCR amplification of the 18S and 28S rDNA genes. Combined 18S and 28S phylogeny of sequences obtained from single cells shows that Radiolaria is divided into two main lineages: Polycystina (Spumellaria+Nassellaria) and Spasmaria (Acantharia+Taxopodida). Further we show with high support that Foraminifera groups within Radiolaria supporting the Retaria hypothesis.     

New insights into relationships between active and dormant organisms,phylogenetic diversity and ecosystem productivity

Marine microbes make up a key part of ocean food webs and drive ocean chemistry through a range of metabolic processes. A fundamental question in ecology is whether the diversity of organisms in a community shapes the ecological functions of that community. While there is substantial evidence to support a positive link between diversity and ecological productivity for macro‐organisms in terrestrial environments, this relationship has not previously been verified for marine microbial communities. One factor complicating the understanding of this relationship is that many marine microbes are dormant and are easily dispersed by ocean currents, making it difficult to ensure that the organisms found in a given environmental sample accurately reflect processes occurring in that environment. Another complication is that, due to microbes great range of genotypic and phenotypic variability, communities with distantly related species may have greater range of metabolic functions than communities have the same richness and evenness, but in which the species present are more closely related to each other. In this issue of Molecular Ecology, Galand et al. (2015) provide compelling evidence that the most metabolically active communities are those in which the nondormant portion of the microbial community has the highest phylogenetic diversity. They also illustrate that focusing on the active portion of the community allows for detection of temporal patterns in community structure that would not be otherwise evident. The authors’ point out that the presence of many dormant organisms that do not contribute to ecosystem functioning is a feature that makes microbial ecosystems fundamentally different from macro‐ecosystems and that this difference needs to be accounted for in microbial ecology theory.     

海洋酸化效应对海水鱼类的综合影响评述

人类活动引起的大气CO2浓度的升高,除了使全球温度升高外,导致的另一个严重生态问题——海洋酸化(Ocean acidification,OA),受到社会各界包括科研界的高度重视,该领域的大部分研究结果都是在近十年才发表出来的,目前还有很多需要解决的问题。海洋酸化的研究涉及到很多学科的交叉包括化学、古生物学、生态学、生物地球化学等等。在生物学领域,海洋酸化主要围绕敏感物种,例如由碳酸钙形成贝壳或外骨骼的贝类,珊瑚礁群体等。鱼类作为海洋脊椎动物的代表生物类群,自身具有一定的酸碱平衡调节能力,但相关海洋酸化方向的研究并不是很多。尽管人们对于海洋酸化对鱼类的影响了解甚少,这并不说明海洋酸化对鱼类没有作用或者效应小,在相关研究逐步展开的同时,发现鱼类同样受到海洋酸化的危害,几乎涉及到鱼类整个生活史和几乎大部分生理过程,尤其是早期生活史的高度敏感。因此就目前国内外对此领域研究结果做综述,以期待业界同行能够对海水鱼类这个大的类群引起重视。     

Ramesh Gulati: a personal approach,based on his retirement lecture

Historical and modern migrations and dispersal of most marine organisms (intertidal, benthic, meiofaunal, planktonic, nektonic, or neustonic) are classically interpreted in terms of their natural dispersal potential. Exceptions are introduced species, largely recognized since the 19th century, known to have been transported by human activities. However, humans were transporting species along coastlines and across oceans for millennia and centuries prior to the advent of the first biological surveys. Thus, the presumptive natural distributions of many species may be questioned. Reviewed here are some basic concepts about invasions of non-native species. Human activities move species isolated in time and space from other oceans or continents, and thus human-mediated transport does not simply speed up natural dispersal processes. Both past and modern-day invasions are often overlooked, leading to an underestimation of the scale of invasion diversity and impact. Because vectors, donor regions, and recipient regions change over time, invasions will continue along long-standing but un-managed corridors. The impact of most invasions has never been studied and, therefore, it is not possible to conclude that most invasions have no impact, nor is it generally possible to say that invasions have become `integrated' into a community or ecosystem in ecological time. Finally, invasions in the ocean are not limited to harbours and ports, but are found in a wide variety of marine habitats, ranging from the open ocean continental shelf to exposed rocky shores. The existence of human-mediated vectors has created extraordinary challenges to our understanding and interpretation of the ecology, biogeography, evolutionary biology, and conservation biology of marine communities.     

A review of bipolarity concepts: History and examples from Radiolaria and Medusozoa (Cnidaria)

Bipolarity, its history and general interpretation are investigated and discussed herein. Apart from the classical view, namely that a bipolar distribution is a peculiar biogeographical phenomenon, we propose that it is ecologically controlled too. This approach was used for bipolarity assessment within the following groups: Phaeodaria, Nassellaria, Spumellaria (Radiolaria) and Medusozoa (Cnidaria). We recognize 46 bipolar radiolarian species and three radiolarian genera. However, although species concepts in radiolarians are relatively stable and well known, the high-rank taxonomy of radiolarians is still not well defined. Caution should therefore be taken in the interpretation of distribution data at a taxonomic level higher than the species. In the Medusozoa, bipolarity is observed for 23 species and 32 genera. The different ways in which bipolarity can develop are discussed under the different groups, but preference has been given to the recent and most probable routes of migration. In our investigation of the bipolarity phenomenon, we reviewed more than 400 articles dealing with taxonomy, ecology and biogeography of the modern fauna in both groups.     

Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean

Despite the ecological importance of marine pico-size eukaryotes, the study of their in situ diversity using molecular tools started just a few years ago. These studies have revealed that marine picoeukaryotes are very diverse and include many novel taxa. However, the amount and structure of their phylogenetic diversity and the extent of their sequence novelty still remains poorly known, as a systematic analysis has been seldom attempted. In this study, we use a coherent and carefully curated data set of 500 published 18S ribosomal DNA sequences to quantify the diversity and novelty patterns of picoeukaryotes in the Indian Ocean. Our phylogenetic tree showed many distant lineages. We grouped sequences in OTUs (operational taxonomic units) at discrete values delineated by pair-wise Jukes–Cantor (JC) distances and tree patristic distances. At a distance of 0.01, the number of OTUs observed (237/242; using JC or patristic distances, respectively) was half the number of sequences analyzed, indicating the existence of microdiverse clusters of highly related sequences. At this distance level, we estimated 600–800 OTUs using several statistical methods. The number of OTUs observed was still substantial at higher distances (39/82 at 0.20 distance) suggesting a large diversity at high-taxonomic ranks. Most sequences were related to marine clones from other sites and many were distant to cultured organisms, highlighting the huge culturing gap within protists. The novelty analysis indicated the putative presence of pseudogenes and of truly novel high-rank phylogenetic lineages. The identified diversity and novelty patterns among marine picoeukaryotes are of great importance for understanding and interpreting their ecology and evolution.     

The Radiolarian biotic response during OAE2. A high-resolution study across the Bonarelli level at Bottaccione (Gubbio, Italy)

In order to improve our understanding of the radiolarian biotic response and the palaeoceanographic changes associated with the Late Cenomanian oceanic anoxic event (OAE2), a high-resolution radiolarian study was carried out across the Bonarelli level at its typical locality (Bottaccione section, central Italy). Our results confirm that a drastic radiolarian faunal change took place during the OAE2. The radiolarian turnover took place within the median part of the Bonarelli level, associated with an interval of high organic matter preservation, but relatively low values of silica. Therefore, this part constitutes a critical period in the evolutionary history of Radiolaria. A synthesis of all data available in the Umbria-Marche basin suggests that the lower part of the Bonarelli level (and underlying limestones) records mainly radiolarian extinctions (ca. 41%), while its upper part (and overlying limestones) records mainly first occurrences (ca. 35%). Our results improve understanding of the paleoecology of the family Saturnalidae, which would seem to prefer oligotrophic environments.     

Diversity and genomics of Antarctic marine micro-organisms

Marine bacterioplanktons are thought to play a vital role in Southern Ocean ecology and ecosystem function, as they do in other ocean systems. However, our understanding of phylogenetic diversity, genome-enabled capabilities and specific adaptations to this persistently cold environment is limited. Bacterioplankton community composition shifts significantly over the annual cycle as sea ice melts and phytoplankton bloom. Microbial diversity in sea ice is better known than that of the plankton, where culture collections do not appear to represent organisms detected with molecular surveys. Broad phylogenetic groupings of Antarctic bacterioplankton such as the marine group I Crenarchaeota, alpha-Proteobacteria (Roseobacter-related and SAR-11 clusters), gamma-Proteobacteria (both cultivated and uncultivated groups) and Bacteriodetes-affiliated organisms in Southern Ocean waters are in common with other ocean systems. Antarctic SSU rRNA gene phylotypes are typically affiliated with other polar sequences. Some species such as Polaribacter irgensii and currently uncultivated gamma-Proteobacteria (Ant4D3 and Ant10A4) may flourish in Antarctic waters, though further studies are needed to address diversity on a larger scale. Insights from initial genomics studies on both cultivated organisms and genomes accessed through shotgun cloning of environmental samples suggest that there are many unique features of these organisms that facilitate survival in high-latitude, persistently cold environments.     

Molecular phylogeny of solitary shell-bearing Polycystinea (Radiolaria)

The phylogeny of the Family Spongodiscidae (polycystine Radiolaria), which includes Dictyocoryne profunda Ehrenberg, Dictyocoryne truncatum (Ehrenberg) and Spongaster tetras Ehrenberg, was examined using 18S ribosomal DNA (small-subunit ribosomal DNA) sequence analysis. Three types of tree construction methods, the neighbor joining (NJ), maximum parsimony (MP), and maximum likelihood (ML) methods, were used to infer the phylogenetic relationships of the polycystine and acantharian Radiolaria among eukaryotes. The obtained 18S rDNA molecular phylogenetic tree argues for the monophyly of the two groups. Furthermore, the Polycystinea is divided into at least two distinct lineages consisting of: (1) colonial and skeletonless Polycystinea, including Thalassicollidae, Collospaeridae, and Sphaerozoidae; and (2) shell-bearing solitary Polycystinea, including Spongodiscidae. The Polycystinea thus show a paraphyly among Radiolaria. Moreover, the monophyly of the clade including the acantharians and the spongodiscid polycystines was supported by bootstrap values, which were 94%, 53%, and 59% in the NJ, MP, and ML analyses, respectively. This lineage is characterized by having latticed or spongy skeletons of different chemical composition, namely SiO₂ (Class Polycystinea) or SrSO₄ (Class Acantharea). According to the present taxonomic scheme, the Acantharea and the Polycystinea have not been placed in different classes, but the results of our molecular study show the opposite. We therefore suggest, based on the monophyly of the two clades, that a new taxonomic group of Radiolaria can be established. Our molecular data also suggest that the currently used radiolarian taxonomic system may need serious revisions.     

Palaeoecology and evolution of Mesozoic salinity-controlled benthic macroinvertebrate associations

Salinity-controlled benthic macroinvertebrate associations are typical of many Mesozoic marginally marine environments. They can be recognized by abiotic criteria (e.g., environmental setting, specific autigenic minerals), by biotic criteria (faunal composition, diversity, shell morphology, size-frequency histograms, taphonomic features, associated micro fauna and microflora), and by isotope geochemistry of shells. Although salinity-controlled associations must have been widespread in the European German Triassic, very little is known about their ecology. They appear to have been dominated by the bivalve Unionites and the brachiopod Lingula. In the Jurassic, brackish-water associations are characterized by bivalves, in particular neomiodontids, corbulids, mytilids, bakevelliids, isognomonids, and oysters. In the Cretaceous, in addition, corbiculid bivalves and gastropods become increasingly abundant. Salinity-controlled benthic macroinvertebrate associations can be used to reconstruct salinity regimes of ancient environments, but emphasis should be placed on an integrated sedimentological and ecological approach, as salinity is rarely the only parameter influencing faunal composition and diversity. Although the species composition of salinity-controlled benthic associations changes distinctly through time, the composition of morphotypes remains surprisingly constant throughout the Mesozoic and up to the Recent, evidence of a conservative evolution of benthic faunas within marginal marine high-stress environments. □ Salinity, benthic associations, palaeoecology, Mesozoic.     

The deep-sea copepod fauna of the Southern Ocean: patterns and processes

In recent years, much attention has been paid to the Antarctic epipelagic fauna, as a result of the desire to increase our knowledge of ecosystem function and resource management. Unfortunately, our understanding of the polar pelagic deep-sea has not progressed as fast, and in common with many other parts of the world's deep ocean, knowledge is still fragmentary. As yet, we have an incomplete but evolving knowledge of species presence and distribution, but very little idea of how the extreme seasonality seen in the Southern Ocean might influence the deep-water fauna. An examination is made of species distribution and diversity, in relation to the latitudinal cline seen in many benthic groups, and the historical perspective offered by changing circulation patterns and sea temperature through geological time. Although a number of important frontal systems are found within the circumpolar Southern Ocean, the boundary is marked by the Sub-Tropical Convergence, which appears to be the major biogeographic boundary between it and surrounding provinces. Evidence for seasonality in various families is reviewed in light of what we know and can infer about their biology and particularly in respect of their bathymetric distribution, which in some groups appears to change with latitude.     

Rapid speciation and ecological divergence in the American seven-spined gobies (Gobiidae,Gobiosomatini) inferred from a molecular phylogeny

Abstract.— The American seven-spined gobies (Gobiidae, Gobiosomatini) are highly diverse both in morphology and ecology with many endemics in the Caribbean region. We have reconstructed a molecular phylogeny of 54 Gobio-somatini taxa (65 individuals) based on a 1646-bp region that includes the mitochondrial 12S rRNA, tRNA-Val, and 16S rRNA genes. Our results support the monophyly of the seven-spined gobies and are in agreement with the existence of two major groups within the tribe, the Gobiosoma group and the Microgobius group. However, they reject the monophyly of some of the Gobiosomatini genera. We use the molecular phylogeny to study the dynamics of speciation in the Gobiosomatini by testing for departures from the constant speciation rate model. We observe a burst of speciation in the early evolutionary history of the group and a subsequent slowdown. Our results show a split among clades into coastal-estuarian, deep ocean, and tropical reef habitats. Major habitat shifts account for the early significant acceleration in lineage splitting and speciation rate and the initial divergence of the main Gobiosomatini clades. We found that subsequent diversification is triggered by behavior and niche specializations at least in the reef-associated clades. Overall, our results confirm that the diversity of Gobiosomatini has arisen during episodes of adaptive radiation, and emphasize the importance of ecology in marine speciation.     

Beyond the beaten path: improving natural products bioprospecting using an eco-evolutionary framework – the case of the octocorals

Marine natural products (NPs) represent an impressive source of novel bioactive molecules with major biotechnological applications. Nevertheless, the usual chemical and applied perspective leading most of bioprospecting projects come along with various limitations blurring our understanding of the extensive marine chemical diversity. Here, we propose several guidelines: (i) to optimize bioprospecting and (ii) to refine our knowledge on marine chemical ecology focusing on octocorals, one of the most promising sources of marine NPs. We identified a significant phylogenetic bias in the octocoral bioprospecting, which calls for the development of a concerted discovery strategy. Given the gap existing between the number of isolated NPs and the knowledge regarding their functions, we provide an ecologically centered workflow prioritizing biological function ahead of chemical identification. Furthermore, we illustrate how -omic technologies should rapidly increase our knowledge on solving different aspects of the ecology and evolution of marine NPs.